1
|
Khandia R, Pandey MK, Khan AA, Baklanov I, Alanazi AM, Nepali P, Gurjar P, Choudhary OP. Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization. Ann Med Surg (Lond) 2024; 86:1359-1369. [PMID: 38463112 PMCID: PMC10923308 DOI: 10.1097/ms9.0000000000001465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 03/12/2024] Open
Abstract
Haem oxygenase-1 (HO-1) is a ubiquitously expressed gene involved in cellular homoeostasis, and its imbalance in expression results in various disorders. To alleviate such disorders, HO-1 gene expression needs to be modulated. Codon usage bias results from evolutionary forces acting on any nucleotide sequence and determines the gene expression. Like codon usage bias, codon pair bias also exists, playing a role in gene expression. In the present study, HO-1 gene was recoded by manipulating codon and codon pair bias, and four such constructs were made through codon/codon pair deoptimization and codon/codon pair optimization to reduce and enhance the HO-1 gene expression. Codon usage analysis was done for these constructs for four tissues brain, heart, pancreas and liver. Based on codon usage in different tissues, gene expression of these tissues was determined in terms of the codon adaptation index. Based on the codon adaptation index, minimum free energy, and translation efficiency, constructs were evaluated for enhanced or decreased HO-1 expression. The analysis revealed that for enhancing gene expression, codon pair optimization, while for reducing gene expression, codon deoptimization is efficacious. The recoded constructs developed in the study could be used in gene therapy regimens to cure HO-1 over or underexpression-associated disorders.
Collapse
Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, MP, India
| | - Megha Katare Pandey
- Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, MP, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Igor Baklanov
- Department of Philosophy, North Caucasus Federal University, Pushkina, Stavropol, Russia
| | - Amer M. Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Prakash Nepali
- Bhimad Primary Health Care Center, Government of Nepal, Tanahun, Nepal
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda, Punjab, India
| |
Collapse
|
2
|
Lee MA, You SH, Jayaramaiah U, Shin EG, Song SM, Ju L, Kang SJ, Cho SH, Hyun BH, Lee HS. Evaluation and Determination of a Suitable Passage Number of Codon Pair Deoptimized PRRSV-1 Vaccine Candidate in Pigs. Viruses 2023; 15:v15051071. [PMID: 37243157 DOI: 10.3390/v15051071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is major economic problem given its effects on swine health and productivity. Therefore, we evaluated the genetic stability of a codon pair de-optimized (CPD) PRRSV, E38-ORF7 CPD, as well as the master seed passage threshold that elicited an effective immune response in pigs against heterologous virus challenge. The genetic stability and immune response of every 10th passage (out of 40) of E38-ORF7 CPD was analyzed through whole genome sequencing and inoculation in 3-week-old pigs. E38-ORF7 CPD passages were limited to 20 based on the full-length mutation analysis and animal test results. After 20 passages, the virus could not induce antibodies to provide effective immunity and mutations accumulated in the gene, which differed from the CPD gene, presenting a reason for low infectivity. Conclusively, the optimal passage number of E38-ORF7 CPD is 20. As a vaccine, this may help overcome the highly diverse PRRSV infection with substantially enhanced genetic stability.
Collapse
Affiliation(s)
- Min-A Lee
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Su-Hwa You
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Usharani Jayaramaiah
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Eun-Gyeong Shin
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Seung-Min Song
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Lanjeong Ju
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Seok-Jin Kang
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Sun-Hee Cho
- Department of Animal Veterinary Development, BioPOA, Hwaseong-si 18469, Republic of Korea
| | - Bang-Hun Hyun
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| | - Hyang-Sim Lee
- Viral Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si 39660, Republic of Korea
| |
Collapse
|
3
|
Trimpert J, Dietert K, Firsching TC, Ebert N, Thi Nhu Thao T, Vladimirova D, Kaufer S, Labroussaa F, Abdelgawad A, Conradie A, Höfler T, Adler JM, Bertzbach LD, Jores J, Gruber AD, Thiel V, Osterrieder N, Kunec D. Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding. Cell Rep 2021; 36:109493. [PMID: 34320400 PMCID: PMC8289629 DOI: 10.1016/j.celrep.2021.109493] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/21/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022] Open
Abstract
Safe and effective vaccines are urgently needed to stop the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We construct a series of live attenuated vaccine candidates by large-scale recoding of the SARS-CoV-2 genome and assess their safety and efficacy in Syrian hamsters. Animals were vaccinated with a single dose of the respective recoded virus and challenged 21 days later. Two of the tested viruses do not cause clinical symptoms but are highly immunogenic and induce strong protective immunity. Attenuated viruses replicate efficiently in the upper but not in the lower airways, causing only mild pulmonary histopathology. After challenge, hamsters develop no signs of disease and rapidly clear challenge virus: at no time could infectious virus be recovered from the lungs of infected animals. The ease with which attenuated virus candidates can be produced and administered favors their further development as vaccines to combat the ongoing pandemic.
Collapse
Affiliation(s)
- Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Kristina Dietert
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany; Tiermedizinisches Zentrum für Resistenzforschung, Freie Universität Berlin, Berlin, Germany
| | | | - Nadine Ebert
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | | | - Susanne Kaufer
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Andelé Conradie
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Thomas Höfler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Julia M Adler
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Luca D Bertzbach
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Achim D Gruber
- Institut für Tierpathologie, Freie Universität Berlin, Berlin, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nikolaus Osterrieder
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
4
|
Le Nouën C, McCarty T, Brown M, Smith ML, Lleras R, Dolan MA, Mehedi M, Yang L, Luongo C, Liang B, Munir S, DiNapoli JM, Mueller S, Wimmer E, Collins PL, Buchholz UJ. Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure. Proc Natl Acad Sci U S A 2017; 114:E386-95. [PMID: 28049853 DOI: 10.1073/pnas.1619242114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recoding viral genomes by numerous synonymous but suboptimal substitutions provides live attenuated vaccine candidates. These vaccine candidates should have a low risk of deattenuation because of the many changes involved. However, their genetic stability under selective pressure is largely unknown. We evaluated phenotypic reversion of deoptimized human respiratory syncytial virus (RSV) vaccine candidates in the context of strong selective pressure. Codon pair deoptimized (CPD) versions of RSV were attenuated and temperature-sensitive. During serial passage at progressively increasing temperature, a CPD RSV containing 2,692 synonymous mutations in 9 of 11 ORFs did not lose temperature sensitivity, remained genetically stable, and was restricted at temperatures of 34 °C/35 °C and above. However, a CPD RSV containing 1,378 synonymous mutations solely in the polymerase L ORF quickly lost substantial attenuation. Comprehensive sequence analysis of virus populations identified many different potentially deattenuating mutations in the L ORF as well as, surprisingly, many appearing in other ORFs. Phenotypic analysis revealed that either of two competing mutations in the virus transcription antitermination factor M2-1, outside of the CPD area, substantially reversed defective transcription of the CPD L gene and substantially restored virus fitness in vitro and in case of one of these two mutations, also in vivo. Paradoxically, the introduction into Min L of one mutation each in the M2-1, N, P, and L proteins resulted in a virus with increased attenuation in vivo but increased immunogenicity. Thus, in addition to providing insights on the adaptability of genome-scale deoptimized RNA viruses, stability studies can yield improved synthetic RNA virus vaccine candidates.
Collapse
|